using Kallisto, salmon DESeq2, edgeR
kallisto to DESeq2_another ref
Ⅰ. Preparation process
Ⅱ. In Linux
Ⅲ. In R - to DESeq2 or edgeR
Ⅳ. In R - visualize
- SRA-Toolkit download – https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
1.1. mkdir download -> cd download
1.2. wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.2/sratoolkit.3.0.2-ubuntu64.tar.gz
1.3. tar –zxvf sratoolkit.3.0.2-ubuntu64.tar.gz
1.4. cd sratoolkit.3.0.2-ubuntu64/bin
1.5. pwd
1.6. export PATH=$PATH:'$pwd'
# convert to environment variable
case1 echo "export PATH=$PATH:$pwd" >> ~/.bashrc >> source ~/.bashrc
case2 cd >> vi .bashrc >> add 'export PATH=$PATH:$pwd' in the last line
- RNAseq program download
2.1 conda install -c bioconda kallisto
2.2 conda install -c bioconda salmon
- Creating Metadata
3.1 Go to NCBI
3.2 Search 'Oryza sativa' and filtering (Libarylayout = Paired, LibrarySelection = cDNA, Instrument = Illuminihiseq/ Illumine nova seq 6000/ next seq 500, Organism = Oryza sativa Japonica...etc)
3.3 click 'send to' > select 'run selector' click 'go' > download(metadata) > open as xlsx file > data select